* Why did the judge put Michael in the same jail as his brother? Isn't that awfully ''nice'' of her? Maybe a little ''too'' nice?
** [[{{Handwave}} Handwaved]] in an early season 1 episode: since Michael and Lincoln have different surnames and didn't bring it up, people just didn't realise they were brothers. When Michael ''does'' bring it up later, it causes all kinds of problems.
** It was also mentioned in the pilot that it was part of his plea bargain to be able to go to Fox River which he claimed he wanted because it was close to Chicago.
*** Specifically, Michael fired his gun(at no one) in his fake bank robbery, to qualify for felony charges and high security imprisonment. Then had his lawyer argue that for health reasons(something to do with his sinuses) he had to be in Chicago. He literally planned for EVERYTHING and This Troper firmly believes he'd have had a contigency if the court room gamble didn't work. The actual Fridge Logic applies when you wonder why a man accused of killing the Vice Presidents Brother would be in what appears to be a regular, even if Federal prison. Wouldn't he be placed...I dont know, but elsewhere?
*** This troper recalls Veronica saying (at Michael's sentencing) that Fox River was a top security facility, and placing him there was uncalled for. So your point would make sense for Michael, not Lincoln.
** Also, technically brothers can go to the same prison. (Okay, you would think one would take more care for one who killed the VP's brother, but still.) What is [[{{Handwave}} handwaved]] is that he'd first be put into a prison for an evaluation on where he'd be sent, probably for ninety days. (California is ninety days, not sure about Illinois.) And that prisoner requests of location aren't always (or usually) honored.
** The person who least makes sense at that prison would be Tweener. If he really only stole a baseball card (no matter how much it was worth) with no violence, he probably would have served in county. If he had a few petty theft priors in his background, he may have gone to prison, but very doubtful a high security prison. Then again, considering the large amounts of WillingSuspensionOfDisbelief you need to ignore all the FridgeLogic moments on this show, this is hardly the worst.
*** The actors [[{{LampshadeHanging}} lampshaded]] this more than a few times in interviews.
-->'''Creator/WentworthMiller''': The show is completely preposterous. But that aside, it's a great ride.
* In the bonus episodes: [[spoiler:Michael's death seemed unnecesarry, given that he'd had the forethought to bring a back pack into the prison with some equipment, doesn't it make sense that he was aware fo the possible electrocution (which has was because he discussed it with mahone earlier) and so would have packed some kind of insulating handware as way of a non lethal back up plan?]].
* So, the FBI wants to recruit Michael and his pals to take down the [[TheSyndicate the evil corporation that runs America from the shadows]] with some off-the-wall plan, right? Having Michael on the team makes perfect sense when you consider his ingenious prison break, but...are we really supposed to believe that the best team that the FBI could dredge up consists of a burned-out petty thug from Chicago, some dude who got arrested for holding up a convenience store one time, a white-trash former prison guard who couldn't pass a cop's exam and still lives with his mom, a mentally unstable FBI agent who's addicted to pills, and a prison doctor who happens to be a recovering morphine addict? For a crazy scheme to steal data-cards from Evil Inc., wouldn't it make more sense to recruit...I don't know...maybe a mercenary or two? Or a professional thief serving prison time? It's the FBI after all. They could use their imaginations...
** First of all, it's not the FBI, it's Homeland Security. Second, they wanted a team that was off the books, not to mention expendable. And third, and more importantly, they needed Michael Scofield. He was the key. The others were only there for Scofield's benefit. No one else was as smart as him and no one else could have pulled off what he did.
* The timeline is ALL out of whack. Based on Lincoln's execution dates, it seems like a maximum of six weeks could have passed between Michael entering Fox River and the break-out. However, in this period, they pass through a period of 100 degree days, then it snows, and then they go all the way to Pope's wedding anniversary in June. It's the Chicago area, so anything's possible, but it strongly suggests that they've somehow gone through four seasons in less than two months. Not to mention that Michael [[spoiler: dies in "The Final Break" on November 4, 2005 - suggesting that the entire series up to the four-year time skip happened over the course of three months.]]
* Was it ever explained why The Company needed to fake the VP's brother's death and frame Linc for it?
** Barely. It was touched on slightly in the first season: [[spoiler: Linc's father, Aldo Burrows, was a Company operative who went into hiding after he tried to leak the details about a new energy source being developed by Steadman's company to the public. They wanted to use Aldo's son as leverage against him, so they faked Steadman's murder and got Linc put on death row for it. Also, Linc had a job at a warehouse used by Steadman's company--he had been fired from the job on the day of Steadman's murder, so they thought he would seem like a likely suspect if Steadman ever wound up dead]]. In theory, [[spoiler: if Aldo had actually surrendered to the Company early on, the Company might have pulled strings to get Linc released]].